Allorecognition, the ability of an organism to distinguish kin from non-kin, or self from non-self, has been studied extensively in a group of invertebrate chordates, the colonial ascidians called botryllids (Subphylum Tunicata, Class Ascidiacea, Family Styelidae).  When two conspecific botryllid colonies come in contact, there are two potential outcomes to an allorecognition reaction: fusion or rejection. The rejection outcome of allorecognition varies by species and has been classified by type (referred to as R-type). R-type is defined according to how far the fusion process progresses before the rejection begins, since the rejection reaction appears as an interference of the fusion process. Here, we map evolution of R-types onto an extended and robust phylogeny of the botryllids. In this study, we have reconstructed the largest phylogenomic tree of botryllids, including 98 samples and more than 40 different species, and mapped on it nine of the 12 species for which the R-type is known. Based on the R-type known in a single outgroup species (Symplegma reptans), we infer that at least R-Type B and E are ancestral to the Botrylloides/Botryllus group. However, based on the most basal botryllid clade, the R-Ttype D could also be considered the botryllid ancestral R-type. The R-Type A species are all clustered together and certainly evolved later than R-Type B and E. Our phylogenomic tree has been built on 200 nuclear loci, but it also takes into account the results of species delimitation analyses based on the mitochondrial COI gene and careful morphological analyses of the samples. The implementation of this integrated taxonomic approach, combining morphological as well as nuclear and mitochondrial data, has allowed the description of six new species and the identification of a number of putative unnamed taxa.  Our results demonstrate the existence of an unexplored hidden diversity within botryllids.